rs659527

Positions:

• chr9-32527326-A-G
• chr9-32527326-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000681750.1(ENSG00000288684):​c.-45+23448T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 151,826 control chromosomes in the GnomAD database, including 28,737 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.61 (28737 hom., cov: 30)
• Consequence: ENSG00000288684 ENST00000681750.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.848

Genes affected

ENSG00000288684 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32527326A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000288684	ENST00000681750.1	c.-45+23448T>C		intron_variant				ENSP00000506413.1
ENSG00000288684	ENST00000680198.1	c.198+23448T>C		intron_variant				ENSP00000505143.1

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93045 AN: 151708 Hom.: 28704 Cov.: 30

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.609

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.613 AC: 93117 AN: 151826 Hom.: 28737 Cov.: 30 AF XY: 0.607 AC XY: 45010 AN XY: 74186

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.527

Gnomad4 ASJ AF: 0.640

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.638

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.603

Alfa AF: 0.631 Hom.: 13322

Bravo AF: 0.611

Asia WGS AF: 0.523 AC: 1821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.90

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs659527; hg19: chr9-32527324;